You need to make sure that the things you create are assigned to the Character Set. If you select your Character Set, and under Repeater Profile it doesn't have a sub-item for the one you created, it will not be active.

Repeater will not adhere to FTL -- if you want to use FTL, you will need to make Mapped Keys for each FTL'd key, and make sure they have FTL enabled in order to use the FTL modifiers. Usually with FTL you want automatic assist (the T in FTL being Targetless), so that's normally not an issue -- you would need a macro for each one anyway. So, for example, if you're playing warlocks you might make a World of Warcraft Macro Action for /cast Shadow Bolt, and select "But first, Assist Hot Character" and "... and restore target afterward". The macro is automatically modified for you by the targeting options, to handle FTL.

When I am in combat, I have repeater turned off. I only turn it on when I need the one-to-one functionality it provides (e.g. typing). I activate my abilities with Mapped Keys, generally with World of Warcraft Macro Actions. This way it doesn't matter where the abilities are in my action bars (and maybe they aren't) or what the normal key bindings I have assigned are. I can change any of those things while I play and not break multi-boxing (similarly I can change all of my multi-boxing stuff without affecting solo play).

Some people do it with repeat enabled, and just hit the usual in-game hotkeys. That's fine to do. It's up to you -- as the guide on the site says, there are multiple ways to do things, and whichever one works and feels right to you, is the way you should do it.

Hope this helps -- I'm moving this weekend (Thurs-Sun) so I might not be available when you need help. Highly recommend the chat channel (you can find it via the Help menu in ISBoxer), there's 25-30 people there that have been using ISBoxer for a while, and most of them can answer your questions or help you out if needed.